Applications/Cufflinks

Application Details

• Description: The Cufflinks suite of tools can be used to perform a number of different types of analyses for RNA-Seq experiments. The Cufflinks suite includes a number of different programs that work together to perform these analyses.
• Version: 2.2.1
• Modules: cufflinks/2.2.1
• Licence: Open source (Github)

Usage Examples

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.

It provides the following tools:

• cuffcompare
• cuffdiff
• cufflinks
• cuffmerge
• cuffnorm
• cuffquant
• gffread
• gtf_to_sam

With linkages to the following modules too:

• Bowtie1
• Bowtie2
• Samtools
• Tophat

[username@login01 ~]$ module add cufflinks/2.2.1

#!/bin/bash
#
#SBATCH -J cufflinks-test
#SBATCH -n 1
#SBATCH --ntasks-per-node=2 
#SBATCH --output=output.%j.cufflinks-test
#SBATCH --time=00:10:00

#### SLURM task using 1 Node with 2 Processors per Node cufflinks test to run for 10 minutes.

module purge
module load apps/cufflinks/2.2.1

CUFFLINKS_OUTPUT="${PWD}"

cufflinks --quiet --num-threads $SLURM_NTASKS --output-dir $CUFFLINKS_OUTPUT input.bam

Further Information

• http://cole-trapnell-lab.github.io/cufflinks/

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